Hello,
My simulation involves a polymer chain and a crystal over which the chain
should be crystallized. I want to create walls on four sides of the
simulation box to make sure the chain interacts with only that surface. I
used fixed boundary conditions for all three dimensions and fix
wall/harmonic command to create a wall.
fix walllj chains wall/harmonic xlo -5 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic xhi -95 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zlo -8 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zhi 100 20.0 2.0 12.5 units box
My simulation box dimension:
-6 +96 xlo xhi
-51 +51 ylo yhi
-9 +101 zlo zhi
When I start the simulation, it runs for a while and when the polymer
chain comes too close to the face of my simulation box, it doesn't
interact with the harmonic wall and just pass through it. I get an error
"ERROR on proc 4: Bond atoms 290 291 missing on proc 4 at step 932628
(../neigh_bond.cpp:65)"
Can anyone tell me what my mistake is?
Hello,
My simulation involves a polymer chain and a crystal over which the chain
should be crystallized. I want to create walls on four sides of the
simulation box to make sure the chain interacts with only that surface. I
used fixed boundary conditions for all three dimensions and fix
wall/harmonic command to create a wall.
fix walllj chains wall/harmonic xlo -5 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic xhi -95 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zlo -8 20.0 2.0 12.5 units box
fix walllj chains wall/harmonic zhi 100 20.0 2.0 12.5 units box
My simulation box dimension:
-6 +96 xlo xhi
-51 +51 ylo yhi
-9 +101 zlo zhi
When I start the simulation, it runs for a while and when the polymer
chain comes too close to the face of my simulation box, it doesn't
interact with the harmonic wall and just pass through it. I get an error
"ERROR on proc 4: Bond atoms 290 291 missing on proc 4 at step 932628
(../neigh_bond.cpp:65)"
Can anyone tell me what my mistake is?
you are using the same fix id for all your fix wall commands. this way the
next wall definition will overwrite the previous one and thus your system
has only one wall instead of four. please re-read the documentation for the
fix command carefully: http://lammps.sandia.gov/doc/fix.html
axel.
oh, and you can confirm this, by adding the command “info fixes” to your input and checking the corresponding output. http://lammps.sandia.gov/doc/info.html
axel.